Just bring the GM hammer down on people that are trying to create Sue-like species. 

For me, when I'm drafting a custom species, I strive to pay close attention to the cons and pros that are inherent to the numerous attributes that I might apply to my creation. For example, I was planning on apping in with the [i]Mason's Pride[/i], a veteran shock force comprised entirely of thirty-two primordial, master-crafted gargoyle statues that operate as life support units for dismembered and decrepit human bodies. Armor-like stony skin, an acute resistance to magic, a short-ranged field of otherworldly energies that literally causes demonic entities and malicious spirits to undergo harm, and in possession of enough physical strength to move their six tons of living granite bulk with haste and efficiency (their dimensions I basically cribbed from Michelangelo's [i]David[/i] because of sheer laziness) makes them out as nigh-unbeatable warriors, but if you take into account that their creator is dead and consequently took her knowledge with her to the grave, you now have a 'faction' that cannot replenish its losses whatsoever. It's a doomed collective from the start; raw [i]attrition will[/i] kill them before the RP comes to a close. It's one of Wernher's 'Epic Downfall' moments I guess.

Plus their size makes them shitty for indoor combat. The possibilities are endless. But I like to keep things consistent and realistic to a degree.